51
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Integration and exchange of split dCas9 domains for transcriptional controls in mammalian cells. Nat Commun 2016; 7:13056. [PMID: 27694915 PMCID: PMC5063958 DOI: 10.1038/ncomms13056] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/30/2016] [Indexed: 01/19/2023] Open
Abstract
Programmable and precise regulation of dCas9 functions in response to multiple molecular signals by using synthetic gene circuits will expand the application of the CRISPR-Cas technology. However, the application of CRISPR-Cas therapeutic circuits is still challenging due to the restrictive cargo size of existing viral delivery vehicles. Here, we construct logic AND circuits by integrating multiple split dCas9 domains, which is useful to reduce the size of synthetic circuits. In addition, we engineer sensory switches by exchanging split dCas9 domains, allowing differential regulations on one gene, or activating two different genes in response to cell-type specific microRNAs. Therefore, we provide a valuable split-dCas9 toolkit to engineer complex transcription controls, which may inspire new biomedical applications. Molecular engineering of Cas9 has the potential to expand the application of CRISPR-Cas technology. Here, Ma et al. show that dCas9 can be split and reconstituted in human cells and use a domain swapping strategy to engineer custom Cas9-based logic circuits and sensory switches.
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52
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Angelici B, Mailand E, Haefliger B, Benenson Y. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells. Cell Rep 2016; 16:2525-37. [PMID: 27545896 PMCID: PMC5009115 DOI: 10.1016/j.celrep.2016.07.061] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/19/2016] [Accepted: 07/22/2016] [Indexed: 11/02/2022] Open
Abstract
One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators.
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Affiliation(s)
- Bartolomeo Angelici
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, 4058 Basel, Switzerland
| | - Erik Mailand
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, 4058 Basel, Switzerland
| | - Benjamin Haefliger
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, 4058 Basel, Switzerland
| | - Yaakov Benenson
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, 4058 Basel, Switzerland.
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53
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Synthetic biology — application-oriented cell engineering. Curr Opin Biotechnol 2016; 40:139-148. [DOI: 10.1016/j.copbio.2016.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 01/01/2023]
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54
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Huang C, Du Y, Nabzdyk CS, Ogawa R, Koyama T, Orgill DP, Fu X. Regeneration of hair and other skin appendages: A microenvironment-centric view. Wound Repair Regen 2016; 24:759-766. [PMID: 27256925 DOI: 10.1111/wrr.12451] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 04/20/2016] [Accepted: 05/28/2016] [Indexed: 12/19/2022]
Abstract
Advances in skin regeneration have resulted in techniques and products that have allowed regeneration of both the dermis and epidermis. Yet complete skin regeneration requires the adnexal skin structures. Thus it is crucial to understand the regenerative potential of hair follicles where genetic, nutritional, and hormonal influences have important effects and are critical for skin regeneration. The follicular stem cell niche serves as an anatomical compartment, a structural unit, a functional integrator, and a dynamic regulator necessary to sustain internal homeostasis and respond to outside stimuli. In particular, mechanics such as pressure, compression, friction, traction, stretch, shear, and mechanical wounding can influence hair loss or growth. Relevant niche signaling pathways such as Wnt, bone morphogenetic protein, fibroblast growth factor, Shh, and Notch may yield potential targets for therapeutic interventions.
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Affiliation(s)
- Chenyu Huang
- Department of Plastic, Reconstructive and Aesthetic Surgery, Beijing Tsinghua Changgung Hospital, Medical Center, Tsinghua University, Beijing, China
| | - Yanan Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Christoph S Nabzdyk
- Division of Plastic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rei Ogawa
- Department of Plastic, Reconstructive and Aesthetic Surgery, Nippon Medical School, Tokyo, Japan
| | | | - Dennis P Orgill
- Division of Plastic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xiaobing Fu
- Institute of Basic Medical Science, The General Hospital of PLA, Beijing, China.
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55
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Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat Methods 2016; 13:127-37. [PMID: 26820547 DOI: 10.1038/nmeth.3733] [Citation(s) in RCA: 296] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/16/2015] [Indexed: 02/08/2023]
Abstract
Gene regulation is a complex and tightly controlled process that defines cell identity, health and disease, and response to pharmacologic and environmental signals. Recently developed DNA-targeting platforms, including zinc finger proteins, transcription activator-like effectors (TALEs) and the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 system, have enabled the recruitment of transcriptional modulators and epigenome-modifying factors to any genomic site, leading to new insights into the function of epigenetic marks in gene expression. Additionally, custom transcriptional and epigenetic regulation is facilitating refined control over cell function and decision making. The unique properties of the CRISPR-Cas9 system have created new opportunities for high-throughput genetic screens and multiplexing targets to manipulate complex gene expression patterns. This Review summarizes recent technological developments in this area and their application to biomedical challenges. We also discuss remaining limitations and necessary future directions for this field.
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56
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Ede C, Chen X, Lin MY, Chen YY. Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells. ACS Synth Biol 2016; 5:395-404. [PMID: 26883397 DOI: 10.1021/acssynbio.5b00266] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.
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Affiliation(s)
- Christopher Ede
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Ximin Chen
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Meng-Yin Lin
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Yvonne Y. Chen
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
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57
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Lee HB, Sundberg BN, Sigafoos AN, Clark KJ. Genome Engineering with TALE and CRISPR Systems in Neuroscience. Front Genet 2016; 7:47. [PMID: 27092173 PMCID: PMC4821859 DOI: 10.3389/fgene.2016.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/16/2016] [Indexed: 12/26/2022] Open
Abstract
Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience.
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Affiliation(s)
- Han B Lee
- Neurobiology of Disease Graduate Program, Mayo Graduate School Rochester, MN, USA
| | - Brynn N Sundberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Ashley N Sigafoos
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Karl J Clark
- Neurobiology of Disease Graduate Program, Mayo Graduate SchoolRochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo ClinicRochester, MN, USA
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58
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Ollé-Vila A, Duran-Nebreda S, Conde-Pueyo N, Montañez R, Solé R. A morphospace for synthetic organs and organoids: the possible and the actual. Integr Biol (Camb) 2016; 8:485-503. [PMID: 27032985 DOI: 10.1039/c5ib00324e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.
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Affiliation(s)
- Aina Ollé-Vila
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
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59
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Liu D, Hu R, Palla KJ, Tuskan GA, Yang X. Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:70-7. [PMID: 26896588 DOI: 10.1016/j.pbi.2016.01.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 05/18/2023]
Abstract
Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. This article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation of gene expression, and identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.
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60
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Ma KC, Perli SD, Lu TK. Foundations and Emerging Paradigms for Computing in Living Cells. J Mol Biol 2016; 428:893-915. [DOI: 10.1016/j.jmb.2016.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023]
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61
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Pu J, Chronis I, Ahn D, Dickinson BC. A Panel of Protease-Responsive RNA Polymerases Respond to Biochemical Signals by Production of Defined RNA Outputs in Live Cells. J Am Chem Soc 2015; 137:15996-9. [PMID: 26652972 DOI: 10.1021/jacs.5b10290] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA is an attractive biomolecule for biosensing and engineering applications due to its information storage capacity and ability to drive gene expression or knockdown. However, methods to link chemical signals to the production of specific RNAs are lacking. Here, we develop protease-responsive RNA polymerases (PRs) as a strategy to encode multiple specific proteolytic events in defined sequences of RNA in live mammalian cells. This work demonstrates that RNAP-based molecular recording devices can be deployed for multimodal analyses of biochemical activities or to trigger gene circuits using measured signaling events.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ian Chronis
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Daniel Ahn
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
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62
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Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJK, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods 2015; 12:1051-4. [PMID: 26344044 PMCID: PMC4666719 DOI: 10.1038/nmeth.3580] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/10/2015] [Indexed: 12/18/2022]
Abstract
We demonstrate that by altering the length of Cas9-associated guide RNA (gRNA) we were able to control Cas9 nuclease activity and simultaneously perform genome editing and transcriptional regulation with a single Cas9 protein. We exploited these principles to engineer mammalian synthetic circuits with combined transcriptional regulation and kill functions governed by a single multifunctional Cas9 protein.
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Affiliation(s)
- Samira Kiani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alejandro Chavez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Marcelle Tuttle
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Richard N Hall
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Raj Chari
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Dmitry Ter-Ovanesyan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason Qian
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin W Pruitt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts, USA
| | - Suhani Vora
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joanna Buchthal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Emma J K Kowal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Mohammad R Ebrahimkhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Emergent Behaviors of Integrated Cellular Systems (EBICS), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Institute for Medical Engineering &Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Emergent Behaviors of Integrated Cellular Systems (EBICS), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - George Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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63
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Abstract
Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
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Affiliation(s)
- Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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64
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Synthetic Biology--Toward Therapeutic Solutions. J Mol Biol 2015; 428:945-62. [PMID: 26334368 DOI: 10.1016/j.jmb.2015.08.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023]
Abstract
Higher multicellular organisms have evolved sophisticated intracellular and intercellular biological networks that enable cell growth and survival to fulfill an organism's needs. Although such networks allow the assembly of complex tissues and even provide healing and protective capabilities, malfunctioning cells can have severe consequences for an organism's survival. In humans, such events can result in severe disorders and diseases, including metabolic and immunological disorders, as well as cancer. Dominating the therapeutic frontier for these potentially lethal disorders, cell and gene therapies aim to relieve or eliminate patient suffering by restoring the function of damaged, diseased, and aging cells and tissues via the introduction of healthy cells or alternative genes. However, despite recent success, these efforts have yet to achieve sufficient therapeutic effects, and further work is needed to ensure the safe and precise control of transgene expression and cellular processes. In this review, we describe the biological tools and devices that are at the forefront of synthetic biology and discuss their potential to advance the specificity, efficiency, and safety of the current generation of cell and gene therapies, including how they can be used to confer curative effects that far surpass those of conventional therapeutics. We also highlight the current therapeutic delivery tools and the current limitations that hamper their use in human applications.
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65
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Kopniczky MB, Moore SJ, Freemont PS. Multilevel Regulation and Translational Switches in Synthetic Biology. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2015; 9:485-496. [PMID: 26336145 DOI: 10.1109/tbcas.2015.2451707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In contrast to the versatility of regulatory mechanisms in natural systems, synthetic genetic circuits have been so far predominantly composed of transcriptionally regulated modules. This is about to change as the repertoire of foundational tools for post-transcriptional regulation is quickly expanding. We provide an overview of the different types of translational regulators: protein, small molecule and ribonucleic acid (RNA) responsive and we describe the new emerging circuit designs utilizing these tools. There are several advantages of achieving multilevel regulation via translational switches and it is likely that such designs will have the greatest and earliest impact in mammalian synthetic biology for regenerative medicine and gene therapy applications.
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66
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Beal J. Signal-to-Noise Ratio Measures Efficacy of Biological Computing Devices and Circuits. Front Bioeng Biotechnol 2015; 3:93. [PMID: 26177070 PMCID: PMC4485182 DOI: 10.3389/fbioe.2015.00093] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/15/2015] [Indexed: 11/13/2022] Open
Abstract
Engineering biological cells to perform computations has a broad range of important potential applications, including precision medical therapies, biosynthesis process control, and environmental sensing. Implementing predictable and effective computation, however, has been extremely difficult to date, due to a combination of poor composability of available parts and of insufficient characterization of parts and their interactions with the complex environment in which they operate. In this paper, the author argues that this situation can be improved by quantitative signal-to-noise analysis of the relationship between computational abstractions and the variation and uncertainty endemic in biological organisms. This analysis takes the form of a ΔSNRdB function for each computational device, which can be computed from measurements of a device's input/output curve and expression noise. These functions can then be combined to predict how well a circuit will implement an intended computation, as well as evaluating the general suitability of biological devices for engineering computational circuits. Applying signal-to-noise analysis to current repressor libraries shows that no library is currently sufficient for general circuit engineering, but also indicates key targets to remedy this situation and vastly improve the range of computations that can be used effectively in the implementation of biological applications.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, USA
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67
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Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol 2014; 3:880-91. [PMID: 25360681 PMCID: PMC4277766 DOI: 10.1021/sb5002856] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotic regulatory proteins respond to diverse signals and represent a rich resource for building synthetic sensors and circuits. The TetR family contains >10(5) members that use a simple mechanism to respond to stimuli and bind distinct DNA operators. We present a platform that enables the transfer of these regulators to mammalian cells, which is demonstrated using human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells. The repressors are modified to include nuclear localization signals (NLS) and responsive promoters are built by incorporating multiple operators. Activators are also constructed by modifying the protein to include a VP16 domain. Together, this approach yields 15 new regulators that demonstrate 19- to 551-fold induction and retain both the low levels of crosstalk in DNA binding specificity observed between the parent regulators in Escherichia coli, as well as their dynamic range of activity. By taking advantage of the DAPG small molecule sensing mediated by the PhlF repressor, we introduce a new inducible system with 50-fold induction and a threshold of 0.9 μM DAPG, which is comparable to the classic Dox-induced TetR system. A set of NOT gates is constructed from the new repressors and their response function quantified. Finally, the Dox- and DAPG- inducible systems and two new activators are used to build a synthetic enhancer (fuzzy AND gate), requiring the coordination of 5 transcription factors organized into two layers. This work introduces a generic approach for the development of mammalian genetic sensors and circuits to populate a toolbox that can be applied to diverse applications from biomanufacturing to living therapeutics.
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Affiliation(s)
- Brynne C. Stanton
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Velia Siciliano
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amar Ghodasara
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liliana Wroblewska
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin Clancy
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Axel C. Trefzer
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Jonathan D. Chesnut
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Ron Weiss
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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